6-88118070-T-C

Variant names:

• chr6-88118070-T-C
• rs2146274

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.458 in 151,846 control chromosomes in the GnomAD database, including 16,659 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.46 (16659 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.15
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.518 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.458 AC: 69535 AN: 151728 Hom.: 16658 Cov.: 30

Gnomad AFR AF: 0.525

Gnomad AMI AF: 0.398

Gnomad AMR AF: 0.338

Gnomad ASJ AF: 0.322

Gnomad EAS AF: 0.145

Gnomad SAS AF: 0.364

Gnomad FIN AF: 0.548

Gnomad MID AF: 0.367

Gnomad NFE AF: 0.471

Gnomad OTH AF: 0.412

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.458 AC: 69572 AN: 151846 Hom.: 16659 Cov.: 30 AF XY: 0.455 AC XY: 33792 AN XY: 74204

African (AFR) AF: 0.524 AC: 21699 AN: 41386

American (AMR) AF: 0.337 AC: 5144 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.322 AC: 1119 AN: 3470

East Asian (EAS) AF: 0.145 AC: 748 AN: 5160

South Asian (SAS) AF: 0.363 AC: 1741 AN: 4798

European-Finnish (FIN) AF: 0.548 AC: 5784 AN: 10548

Middle Eastern (MID) AF: 0.344 AC: 101 AN: 294

European-Non Finnish (NFE) AF: 0.471 AC: 32004 AN: 67932

Other (OTH) AF: 0.415 AC: 869 AN: 2096

Alfa AF: 0.451 Hom.: 7409

Bravo AF: 0.443

Asia WGS AF: 0.281 AC: 976 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.18
DANN	Benign	0.84
PhyloP100		-1.1

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs2146274; hg19: chr6-88827788;